1
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Turlington ZR, Vaz Ferreira de Macedo S, Perry K, Belsky SL, Faust JA, Snider MJ, Hicks KA. Ligand bound structure of a 6-hydroxynicotinic acid 3-monooxygenase provides mechanistic insights. Arch Biochem Biophys 2024; 752:109859. [PMID: 38104959 DOI: 10.1016/j.abb.2023.109859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
6-Hydroxynicotinic acid 3-monooxygenase (NicC) is a bacterial enzyme involved in the degradation of nicotinic acid. This enzyme is a Class A flavin-dependent monooxygenase that catalyzes a unique decarboxylative hydroxylation. The unliganded structure of this enzyme has previously been reported and studied using steady- and transient-state kinetics to support a comprehensive kinetic mechanism. Here we report the crystal structure of the H47Q NicC variant in both a ligand-bound (solved to 2.17 Å resolution) and unliganded (1.51 Å resolution) form. Interestingly, in the liganded form, H47Q NicC is bound to 2-mercaptopyridine (2-MP), a contaminant present in the commercial stock of 6-mercaptopyridine-3-carboxylic acid(6-MNA), a substrate analogue. 2-MP binds weakly to H47Q NicC and is not a substrate for the enzyme. Based on kinetic and thermodynamic characterization, we have fortuitously captured a catalytically inactive H47Q NicC•2-MP complex in our crystal structure. This complex reveals interesting mechanistic details about the reaction catalyzed by 6-hydroxynicotinic acid 3-monooxygenase.
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Affiliation(s)
- Zachary R Turlington
- Department of Chemistry, State University of New York at Cortland, Cortland, NY, 13045, United States
| | | | - Kay Perry
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, IL, United States
| | - Sam L Belsky
- Department of Chemistry, The College of Wooster, Wooster, OH, 44691, United States
| | - Jennifer A Faust
- Department of Chemistry, The College of Wooster, Wooster, OH, 44691, United States
| | - Mark J Snider
- Department of Chemistry, The College of Wooster, Wooster, OH, 44691, United States
| | - Katherine A Hicks
- Department of Chemistry, State University of New York at Cortland, Cortland, NY, 13045, United States.
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2
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Tong Y, Wei Y, Ju Y, Li P, Zhang Y, Li L, Gao L, Liu S, Liu D, Hu Y, Li Z, Yu H, Luo Y, Wang J, Wang Y, Zhang Y. Anaerobic purinolytic enzymes enable dietary purine clearance by engineered gut bacteria. Cell Chem Biol 2023; 30:1104-1114.e7. [PMID: 37164019 DOI: 10.1016/j.chembiol.2023.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/08/2023] [Accepted: 04/17/2023] [Indexed: 05/12/2023]
Abstract
Uric acid, the end product of purine degradation, causes hyperuricemia and gout, afflicting hundreds of millions of people. The debilitating effects of gout are exacerbated by dietary purine intake, and thus a potential therapeutic strategy is to enhance purine degradation in the gut microbiome. Aerobic purine degradation involves oxidative dearomatization of uric acid catalyzed by the O2-dependent uricase. The enzymes involved in purine degradation in strictly anaerobic bacteria remain unknown. Here we report the identification and characterization of these enzymes, which include four hydrolases belonging to different enzyme families, and a prenyl-flavin mononucleotide-dependent decarboxylase. Introduction of the first two hydrolases to Escherichia coli Nissle 1917 enabled its anaerobic growth on xanthine as the sole nitrogen source. Oral supplementation of these engineered probiotics ameliorated hyperuricemia in a Drosophila melanogaster model, including the formation of renal uric acid stones and a shortened lifespan, providing a route toward the development of purinolytic probiotics.
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Affiliation(s)
- Yang Tong
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Department of Chemistry, Tianjin University, Tianjin 300072, P.R. China
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A∗STAR), Singapore 138669, Singapore
| | - Yingjie Ju
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Peishan Li
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Yumin Zhang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300192, P.R. China
| | - Liqin Li
- Tianjin Speerise Challenge Biotechnology Co., Ltd., Zhangjiawo Industrial Park, No. 16 Huiyuan Road, Zhangjiawo Town, Xiqing District, Tianjin 300380, China
| | - Lujuan Gao
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Shengnan Liu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Dazhi Liu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Meining Pharma Inc, 2-401-1, Bldg 8, Huiying Industrial Park, No. 86 West Zhonghuan Road, Tianjin Pilot Free Trade Zone, Tianjin 300308, China
| | - Yiling Hu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Zhi Li
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Hongbin Yu
- Department of Hematology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yunzi Luo
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Jian Wang
- Tianjin Speerise Challenge Biotechnology Co., Ltd., Zhangjiawo Industrial Park, No. 16 Huiyuan Road, Zhangjiawo Town, Xiqing District, Tianjin 300380, China
| | - Yiwen Wang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China.
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Department of Chemistry, Tianjin University, Tianjin 300072, P.R. China.
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3
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Shalaby MA, Fahim AM, Rizk SA. Antioxidant activity of novel nitrogen scaffold with docking investigation and correlation of DFT stimulation. RSC Adv 2023; 13:14580-14593. [PMID: 37197676 PMCID: PMC10183801 DOI: 10.1039/d3ra02393a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 05/02/2023] [Indexed: 05/19/2023] Open
Abstract
Heterocyclic scaffolds are frequently employed in drug development to treat a variety of conditions, including cancers. These substances have the ability to engage covalently or non-covalently with particular residues in the target proteins, inhibiting them. In this study, the formation of N-, S-, and O-containing heterocycles by the interaction of chalcone with nitrogen-containing nucleophiles such as hydrazine, hydroxyl amine, guanidine, urea, and aminothiourea was explored. FT-IR, UV-visible, NMR, and mass spectrometric studies were used to confirm the heterocyclic compounds that were produced. These substances were tested for their antioxidant activity by their capacity to scavenge the artificial radicals 2,2-diphenyl-1-picrylhydrazyl (DPPH). The strongest antioxidant activity was demonstrated by compound 3 (IC50 = 93.4 μM), whereas compound 8 (IC50 = 448.70 μM) had the lowest activity when compared to vitamin C (IC50 141.9 μM). Also, the experimental findings and the docking estimation of these heterocyclic compounds with PDBID:3RP8 were in agreement. Additionally, the compounds' global reactivity characteristics, such as HOMO-LUMO gaps, electronic hardness, chemical potential, electrophilicity index, and Mulliken charges, were identified using DFT/B3LYP/6-31G(d,p) basis sets. The two chemicals that displayed the best antioxidant activity also had their molecular electrostatic potential (MEP) ascertained using DFT simulations.
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Affiliation(s)
- Mona A Shalaby
- Chemistry Department, Faculty of Science, Ain Shams University Abbassia, P.O. 11566 Cairo Egypt
| | - Asmaa M Fahim
- Green Chemistry Department, National Research Centre Dokki, P.O. Box 12622 Cairo Egypt
| | - Sameh A Rizk
- Chemistry Department, Faculty of Science, Ain Shams University Abbassia, P.O. 11566 Cairo Egypt
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4
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Bayrak H, Fahim AM, Yaylaci Karahalil F, Azafad I, Boyraci GM, Taflan E. Synthesis, antioxidant activity, docking simulation, and computational investigation of novel heterocyclic compounds and Schiff Bases from picric acid. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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5
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Discovery and biosynthesis of karnamicins as angiotensin converting enzyme inhibitors. Nat Commun 2023; 14:209. [PMID: 36639377 PMCID: PMC9838390 DOI: 10.1038/s41467-023-35829-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 01/04/2023] [Indexed: 01/15/2023] Open
Abstract
Angiotensin-converting enzyme inhibitors are widely used for treatment of hypertension and related diseases. Here, six karnamicins E1-E6 (1-6), which bear fully substituted hydroxypyridine and thiazole moieties are characterized from the rare actinobacterium Lechevalieria rhizosphaerae NEAU-A2. Through a combination of isotopic labeling, genome mining, and enzymatic characterization studies, the programmed assembly of the fully substituted hydroxypyridine moiety in karnamicin is proposed to be due to sequential operation of a hybrid polyketide synthase-nonribosomal peptide synthetase, two regioselective pyridine ring flavoprotein hydroxylases, and a methyltransferase. Based on AlphaFold protein structures predictions, molecular docking, and site-directed mutagenesis, we find that two pyridine hydroxylases deploy active site residues distinct from other flavoprotein monooxygenases to direct the chemo- and regioselective hydroxylation of the pyridine nucleus. Pleasingly, karnamicins show significant angiotensin-converting enzyme inhibitory activity with IC50 values ranging from 0.24 to 5.81 μM, suggesting their potential use for the treatment of hypertension and related diseases.
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6
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Huynh TN, Stewart V. Purine catabolism by enterobacteria. Adv Microb Physiol 2023; 82:205-266. [PMID: 36948655 DOI: 10.1016/bs.ampbs.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Purines are abundant among organic nitrogen sources and have high nitrogen content. Accordingly, microorganisms have evolved different pathways to catabolize purines and their metabolic products such as allantoin. Enterobacteria from the genera Escherichia, Klebsiella and Salmonella have three such pathways. First, the HPX pathway, found in the genus Klebsiella and very close relatives, catabolizes purines during aerobic growth, extracting all four nitrogen atoms in the process. This pathway includes several known or predicted enzymes not previously observed in other purine catabolic pathways. Second, the ALL pathway, found in strains from all three species, catabolizes allantoin during anaerobic growth in a branched pathway that also includes glyoxylate assimilation. This allantoin fermentation pathway originally was characterized in a gram-positive bacterium, and therefore is widespread. Third, the XDH pathway, found in strains from Escherichia and Klebsiella spp., at present is ill-defined but likely includes enzymes to catabolize purines during anaerobic growth. Critically, this pathway may include an enzyme system for anaerobic urate catabolism, a phenomenon not previously described. Documenting such a pathway would overturn the long-held assumption that urate catabolism requires oxygen. Overall, this broad capability for purine catabolism during either aerobic or anaerobic growth suggests that purines and their metabolites contribute to enterobacterial fitness in a variety of environments.
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Affiliation(s)
- TuAnh Ngoc Huynh
- Department of Food Science, University of Wisconsin, Madison, WI, United States
| | - Valley Stewart
- Department of Microbiology & Molecular Genetics, University of California, Davis, CA, United States.
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7
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The structure of Deinococcus radiodurans transcriptional regulator HucR retold with the urate bound. Biochem Biophys Res Commun 2022; 615:63-69. [DOI: 10.1016/j.bbrc.2022.05.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 04/28/2022] [Accepted: 05/11/2022] [Indexed: 11/18/2022]
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8
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Abstract
Covering: up to the end of July, 2021Anthraquinone-fused enediynes (AFEs) are a subfamily of enediyne natural products. Dynemicin A (DYN A), the first member of the AFE family, was discovered more than thirty years ago. Subsequently, extensive studies have been reported on the mode of action and the interactions of AFEs with DNA using DYN A as a model. However, progress in the discovery, biosynthesis and clinical development of AFEs has been limited for a long time. In the past five years, four new AFEs have been discovered and significant progress has been made in the biosynthesis of AFEs, especially on the biogenesis of the anthraquinone moiety and their tailoring steps. Moreover, the streamlined total synthesis of AFEs and their analogues boosts the preparation of AFE-based linker-drugs, thus enabling the development of AFE-based antibody-drug conjugates (ADCs). This review summarizes the discovery, mechanism of action, biosynthesis, total synthesis and preclinical studies of AFEs.
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Affiliation(s)
- Xiaohui Yan
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, China.
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9
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Bosse MA, Silva MBD, Oliveira NGRMD, Araujo MAD, Rodrigues C, Azevedo JPD, Reis ARD. Physiological impact of flavonoids on nodulation and ureide metabolism in legume plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 166:512-521. [PMID: 34171572 DOI: 10.1016/j.plaphy.2021.06.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/06/2021] [Indexed: 05/20/2023]
Abstract
Legume plants from Fabaceae family (phylogenetic group composed by three subfamilies: Caesalpinioideae, Mimosoideae, and Papilionoideae) can fix atmospheric nitrogen (N2) into ammonia (NH3) by the symbiotic relationship with rhizobia bacteria. These bacteria respond chemotactically to certain compounds released by plants such as sugars, amino acids and organic acids. Root secretion of isoflavonoids acts as inducers for nod genes in rhizobia and ABC transporters and ICHG (isoflavone conjugates hydrolyzing beta-glucosidase) at apoplast are related to the exudation of genistein and daidzein in soybean roots. Biological nitrogen fixation (BNF) occurs inside the nodule by the action of nitrogenase enzyme, which fixes N2 into NH3, which is converted into ureides (allantoin and allantoic acid). In this review, we bring together the latest findings on flavonoids biosynthesis and ureide metabolism in several legume plant species. We emphasize how flavonoids induce nod genes in rhizobia, affecting chemotaxis, nodulation, ureide production, growth and yield of legume plants. Mainly, isoflavonoids daidzein and genistein are responsible for nod genes activation in the rhizobia bacteria. Flavonoids also play an important role during nodule organogenesis by acting as auxin transporter inhibitors in root cells, especially in indeterminate nodules. The ureides are the main N transport form in tropical legumes and they are catabolized in leaves and other sink tissues to produce amino acids and proteins needed for plant growth and yield.
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Affiliation(s)
- Marco Antônio Bosse
- São Paulo State University (UNESP), Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal, SP, Postal Code 14884-900, Brazil
| | | | | | | | - Cleverson Rodrigues
- São Paulo State University (UNESP), Postal Code 15385-000, Ilha Solteira, SP, Brazil
| | | | - André Rodrigues Dos Reis
- São Paulo State University (UNESP), Rua Domingos da Costa Lopes 780, Postal Code 17602-496, Tupã, SP, Brazil.
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10
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Liu Z, Zhao F, Zhao B, Yang J, Ferrara J, Sankaran B, Venkataram Prasad BV, Kundu BB, Phillips GN, Gao Y, Hu L, Zhu T, Gao X. Structural basis of the stereoselective formation of the spirooxindole ring in the biosynthesis of citrinadins. Nat Commun 2021; 12:4158. [PMID: 34230497 PMCID: PMC8260726 DOI: 10.1038/s41467-021-24421-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 06/17/2021] [Indexed: 11/09/2022] Open
Abstract
Prenylated indole alkaloids featuring spirooxindole rings possess a 3R or 3S carbon stereocenter, which determines the bioactivities of these compounds. Despite the stereoselective advantages of spirooxindole biosynthesis compared with those of organic synthesis, the biocatalytic mechanism for controlling the 3R or 3S-spirooxindole formation has been elusive. Here, we report an oxygenase/semipinacolase CtdE that specifies the 3S-spirooxindole construction in the biosynthesis of 21R-citrinadin A. High-resolution X-ray crystal structures of CtdE with the substrate and cofactor, together with site-directed mutagenesis and computational studies, illustrate the catalytic mechanisms for the possible β-face epoxidation followed by a regioselective collapse of the epoxide intermediate, which triggers semipinacol rearrangement to form the 3S-spirooxindole. Comparing CtdE with PhqK, which catalyzes the formation of the 3R-spirooxindole, we reveal an evolutionary branch of CtdE in specific 3S spirocyclization. Our study provides deeper insights into the stereoselective catalytic machinery, which is important for the biocatalysis design to synthesize spirooxindole pharmaceuticals.
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Affiliation(s)
- Zhiwen Liu
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Fanglong Zhao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Boyang Zhao
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Jie Yang
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | | | - Banumathi Sankaran
- Department of Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - B V Venkataram Prasad
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Biki Bapi Kundu
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
| | - George N Phillips
- Department of Biosciences, Rice University, Houston, TX, USA
- Department of Chemistry, Rice University, Houston, TX, USA
| | - Yang Gao
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Tong Zhu
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China.
| | - Xue Gao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA.
- Department of Chemistry, Rice University, Houston, TX, USA.
- Department of Bioengineering, Rice University, Houston, TX, USA.
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11
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Manenda MS, Picard MÈ, Zhang L, Cyr N, Zhu X, Barma J, Pascal JM, Couture M, Zhang C, Shi R. Structural analyses of the Group A flavin-dependent monooxygenase PieE reveal a sliding FAD cofactor conformation bridging OUT and IN conformations. J Biol Chem 2020; 295:4709-4722. [PMID: 32111738 DOI: 10.1074/jbc.ra119.011212] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/26/2020] [Indexed: 02/02/2023] Open
Abstract
Group A flavin-dependent monooxygenases catalyze the cleavage of the oxygen-oxygen bond of dioxygen, followed by the incorporation of one oxygen atom into the substrate molecule with the aid of NADPH and FAD. These flavoenzymes play an important role in many biological processes, and their most distinct structural feature is the choreographed motions of flavin, which typically adopts two distinct conformations (OUT and IN) to fulfill its function. Notably, these enzymes seem to have evolved a delicate control system to avoid the futile cycle of NADPH oxidation and FAD reduction in the absence of substrate, but the molecular basis of this system remains elusive. Using protein crystallography, size-exclusion chromatography coupled to multi-angle light scattering (SEC-MALS), and small-angle X-ray scattering (SEC-SAXS) and activity assay, we report here a structural and biochemical characterization of PieE, a member of the Group A flavin-dependent monooxygenases involved in the biosynthesis of the antibiotic piericidin A1. This analysis revealed that PieE forms a unique hexamer. Moreover, we found, to the best of our knowledge for the first time, that in addition to the classical OUT and IN conformations, FAD possesses a "sliding" conformation that exists in between the OUT and IN conformations. This observation sheds light on the underlying mechanism of how the signal of substrate binding is transmitted to the FAD-binding site to efficiently initiate NADPH binding and FAD reduction. Our findings bridge a gap currently missing in the orchestrated order of chemical events catalyzed by this important class of enzymes.
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Affiliation(s)
- Mahder S Manenda
- Département de Biochimie, de Microbiologie, et de Bio-informatique, PROTEO, Université Laval, Québec G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Marie-Ève Picard
- Département de Biochimie, de Microbiologie, et de Bio-informatique, PROTEO, Université Laval, Québec G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Liping Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Normand Cyr
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Xiaojun Zhu
- Département de Biochimie, de Microbiologie, et de Bio-informatique, PROTEO, Université Laval, Québec G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Julie Barma
- Département de Biochimie, de Microbiologie, et de Bio-informatique, PROTEO, Université Laval, Québec G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - John M Pascal
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Manon Couture
- Département de Biochimie, de Microbiologie, et de Bio-informatique, PROTEO, Université Laval, Québec G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Changsheng Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Rong Shi
- Département de Biochimie, de Microbiologie, et de Bio-informatique, PROTEO, Université Laval, Québec G1V 0A6, Canada .,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
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12
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Fraley AE, Caddell Haatveit K, Ye Y, Kelly SP, Newmister SA, Yu F, Williams RM, Smith JL, Houk KN, Sherman DH. Molecular Basis for Spirocycle Formation in the Paraherquamide Biosynthetic Pathway. J Am Chem Soc 2020; 142:2244-2252. [PMID: 31904957 DOI: 10.1021/jacs.9b09070] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The paraherquamides are potent anthelmintic natural products with complex heptacyclic scaffolds. One key feature of these molecules is the spiro-oxindole moiety that lends a strained three-dimensional architecture to these structures. The flavin monooxygenase PhqK was found to catalyze spirocycle formation through two parallel pathways in the biosynthesis of paraherquamides A and G. Two new paraherquamides (K and L) were isolated from a ΔphqK strain of Penicillium simplicissimum, and subsequent enzymatic reactions with these compounds generated two additional metabolites, paraherquamides M and N. Crystal structures of PhqK in complex with various substrates provided a foundation for mechanistic analyses and computational studies. While it is evident that PhqK can react with various substrates, reaction kinetics and molecular dynamics simulations indicated that the dioxepin-containing paraherquamide L is the favored substrate. Through this effort, we have elucidated a key step in the biosynthesis of the paraherquamides and provided a rationale for the selective spirocyclization of these powerful anthelmintic agents.
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Affiliation(s)
| | - Kersti Caddell Haatveit
- Department of Chemistry and Biochemistry , University of California , Los Angeles , California 90095 , United States
| | | | | | | | | | - Robert M Williams
- Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523 , United States.,University of Colorado Cancer Center , Aurora , Colorado 80045 , United States
| | | | - K N Houk
- Department of Chemistry and Biochemistry , University of California , Los Angeles , California 90095 , United States
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13
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Wang W, Zhu BY, Wang P, Zhang P, Deng WW, Wu FH, Ho CT, Ling TJ, Zhang ZZ, Wan XC, Bao GH. Enantiomeric Trimethylallantoin Monomers, Dimers, and Trimethyltriuret: Evidence for an Alternative Catabolic Pathway of Caffeine in Tea Plant. Org Lett 2019; 21:5147-5151. [PMID: 31247775 DOI: 10.1021/acs.orglett.9b01750] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Racemic trimethylallantoin monomer (1), mesomeric and racemic trimethylallantoin dimers (2 and 3), were isolated from tea. Two pairs of optically pure enantiomers (1a, 1b and 3a, 3b) were separated by chiral column from the two racemes (1 and 3). Their structures were elucidated by a combination of extensive spectroscopic techniques, single-crystal X-ray diffraction, and experimental and calculated electronic circular dichroism. A novel caffeine catabolic pathway was proposed based on the caffeine stable isotopic tracer experiments.
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Affiliation(s)
- Wei Wang
- Natural Products Laboratory, International Joint Laboratory of Tea Chemistry and Health Effects, State Key Laboratory of Tea Plant Biology and Utilization , Anhui Agricultural University , Hefei 230036 , China
| | - Bi-Ying Zhu
- Natural Products Laboratory, International Joint Laboratory of Tea Chemistry and Health Effects, State Key Laboratory of Tea Plant Biology and Utilization , Anhui Agricultural University , Hefei 230036 , China
| | - Pu Wang
- School of Traditional Chinese Pharmacy , China Pharmaceutical University , Nanjing 211198 , China
| | - Peng Zhang
- Natural Products Laboratory, International Joint Laboratory of Tea Chemistry and Health Effects, State Key Laboratory of Tea Plant Biology and Utilization , Anhui Agricultural University , Hefei 230036 , China
| | - Wei-Wei Deng
- Natural Products Laboratory, International Joint Laboratory of Tea Chemistry and Health Effects, State Key Laboratory of Tea Plant Biology and Utilization , Anhui Agricultural University , Hefei 230036 , China
| | - Fei-Hua Wu
- School of Traditional Chinese Pharmacy , China Pharmaceutical University , Nanjing 211198 , China
| | - Chi-Tang Ho
- Natural Products Laboratory, International Joint Laboratory of Tea Chemistry and Health Effects, State Key Laboratory of Tea Plant Biology and Utilization , Anhui Agricultural University , Hefei 230036 , China.,Department of Food Science , Rutgers University , New Brunswick , New Jersey 08901-8520 , United States
| | - Tie-Jun Ling
- Natural Products Laboratory, International Joint Laboratory of Tea Chemistry and Health Effects, State Key Laboratory of Tea Plant Biology and Utilization , Anhui Agricultural University , Hefei 230036 , China
| | - Zheng-Zhu Zhang
- Natural Products Laboratory, International Joint Laboratory of Tea Chemistry and Health Effects, State Key Laboratory of Tea Plant Biology and Utilization , Anhui Agricultural University , Hefei 230036 , China
| | - Xiao-Chun Wan
- Natural Products Laboratory, International Joint Laboratory of Tea Chemistry and Health Effects, State Key Laboratory of Tea Plant Biology and Utilization , Anhui Agricultural University , Hefei 230036 , China
| | - Guan-Hu Bao
- Natural Products Laboratory, International Joint Laboratory of Tea Chemistry and Health Effects, State Key Laboratory of Tea Plant Biology and Utilization , Anhui Agricultural University , Hefei 230036 , China
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14
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Catalytic mechanism for the conversion of salicylate into catechol by the flavin-dependent monooxygenase salicylate hydroxylase. Int J Biol Macromol 2019; 129:588-600. [DOI: 10.1016/j.ijbiomac.2019.01.135] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 01/24/2019] [Accepted: 01/24/2019] [Indexed: 11/17/2022]
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15
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Nakamoto KD, Perkins SW, Campbell RG, Bauerle MR, Gerwig TJ, Gerislioglu S, Wesdemiotis C, Anderson MA, Hicks KA, Snider MJ. Mechanism of 6-Hydroxynicotinate 3-Monooxygenase, a Flavin-Dependent Decarboxylative Hydroxylase Involved in Bacterial Nicotinic Acid Degradation. Biochemistry 2019; 58:1751-1763. [PMID: 30810301 DOI: 10.1021/acs.biochem.8b00969] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
6-Hydroxynicotinate 3-monooxygenase (NicC) is a Group A FAD-dependent monooxygenase that catalyzes the decarboxylative hydroxylation of 6-hydroxynicotinic acid (6-HNA) to 2,5-dihydroxypyridine (2,5-DHP) with concomitant oxidation of NADH in nicotinic acid degradation by aerobic bacteria. Two mechanisms for the decarboxylative hydroxylation half-reaction have been proposed [Hicks, K., et al. (2016) Biochemistry 55, 3432-3446]. Results with Bordetella bronchiseptica RB50 NicC here show that a homocyclic analogue of 6-HNA, 4-hydroxybenzoic acid (4-HBA), is decarboxylated and hydroxylated by NicC with a 420-fold lower catalytic efficiency than is 6-HNA. The 13( V/ K), measured with wild-type NicC by isotope ratio mass spectrometry following the natural abundance of 13C in the CO2 product, is inverse for both 6-HNA (0.9989 ± 0.0002) and 4-HBA (0.9942 ± 0.0004) and becomes negligible (0.9999 ± 0.0004) for 5-chloro-6-HNA, an analogue that is 10-fold more catalytically efficient than 6-HNA. Covalently bound 6-HNA complexes of NicC are not observed by mass spectrometry. Comparative steady-state kinetic and Kd6HNA analyses of active site NicC variants (C202A, H211A, H302A, H47E, Y215F, and Y225F) identify Tyr215 and His47 as critical determinants both of 6-HNA binding ( KdY215F/ KdWT > 240; KdH47E/ KdWT > 350) and in coupling rates of 2,5-DHP and NAD+ product formation ([2,5-DHP]/[NAD+] = 1.00 (WT), 0.005 (Y215F), and 0.07 (H47E)]. Results of these functional analyses are in accord with an electrophilic aromatic substitution reaction mechanism in which His47-Tyr215 may serve as the general base to catalyze substrate hydroxylation and refine the structural model for substrate binding by NicC.
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Affiliation(s)
- Kent D Nakamoto
- Department of Chemistry , The College of Wooster , Wooster , Ohio 44691 , United States
| | - Scott W Perkins
- Department of Chemistry , The College of Wooster , Wooster , Ohio 44691 , United States
| | - Ryan G Campbell
- Department of Chemistry , The College of Wooster , Wooster , Ohio 44691 , United States
| | - Matthew R Bauerle
- Department of Chemistry , The College of Wooster , Wooster , Ohio 44691 , United States
| | - Tyler J Gerwig
- Department of Chemistry , The College of Wooster , Wooster , Ohio 44691 , United States
| | - Selim Gerislioglu
- Department of Chemistry , University of Akron , Akron , Ohio 44325 , United States
| | - Chrys Wesdemiotis
- Department of Chemistry , University of Akron , Akron , Ohio 44325 , United States
| | - Mark A Anderson
- Institute for Enzyme Research, Department of Biochemistry , University of Wisconsin , Madison , Wisconsin 53726 , United States
| | - Katherine A Hicks
- Department of Chemistry , The State University of New York College at Cortland , Cortland , New York 13045 , United States
| | - Mark J Snider
- Department of Chemistry , The College of Wooster , Wooster , Ohio 44691 , United States
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16
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Chen M, Zhang Y, Du Y, Zhao Q, Zhang Q, Wu J, Liu W. Enzymatic competition and cooperation branch the caerulomycin biosynthetic pathway toward different 2,2'-bipyridine members. Org Biomol Chem 2018. [PMID: 28649680 DOI: 10.1039/c7ob01284e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, we characterized CaeB6 as a selective hydroxylase and CaeG1 as an O-methyltransferase in the biosynthesis of the 2,2'-bipyridine natural products caerulomycins (CAEs). The C3-hydroxylation activity of CaeB6 competes with the C4-O-methylation activity of CaeG1 and thereby branches the CAE pathway from a common C4-O-demethylated 2,2'-bipyridine intermediate. CaeG1-catalyzed C4-O-methylation leads to a main route that produces the major product CAE-A in Actinoalloteichus cyanogriseus NRRL B-2194. In contrast, CaeB6-catalyzed C3-hydroxylation results in a shunt route in which CaeG1 causes C4-O-methylation and subsequent C3-O-methylation to produce a series of minor CAE products. These findings provide new insights into the biosynthetic pathway of CAEs and a synthetic biology strategy for the selective functionalization of the 2,2'-bipyridine core.
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Affiliation(s)
- Ming Chen
- State Key Laboratory of Bioorganic and Nature Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
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17
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Marchetti M, Liuzzi A, Fermi B, Corsini R, Folli C, Speranzini V, Gandolfi F, Bettati S, Ronda L, Cendron L, Berni R, Zanotti G, Percudani R. Catalysis and Structure of Zebrafish Urate Oxidase Provide Insights into the Origin of Hyperuricemia in Hominoids. Sci Rep 2016; 6:38302. [PMID: 27922051 PMCID: PMC5138847 DOI: 10.1038/srep38302] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 11/03/2016] [Indexed: 01/24/2023] Open
Abstract
Urate oxidase (Uox) catalyses the first reaction of oxidative uricolysis, a three-step enzymatic pathway that allows some animals to eliminate purine nitrogen through a water-soluble compound. Inactivation of the pathway in hominoids leads to elevated levels of sparingly soluble urate and puts humans at risk of hyperuricemia and gout. The uricolytic activities lost during evolution can be replaced by enzyme therapy. Here we report on the functional and structural characterization of Uox from zebrafish and the effects on the enzyme of the missense mutation (F216S) that preceded Uox pseudogenization in hominoids. Using a kinetic assay based on the enzymatic suppression of the spectroscopic interference of the Uox reaction product, we found that the F216S mutant has the same turnover number of the wild-type enzyme but a much-reduced affinity for the urate substrate and xanthine inhibitor. Our results indicate that the last functioning Uox in hominoid evolution had an increased Michaelis constant, possibly near to upper end of the normal range of urate in the human serum (~300 μM). Changes in the renal handling of urate during primate evolution can explain the genetic modification of uricolytic activities in the hominoid lineage without the need of assuming fixation of deleterious mutations.
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Affiliation(s)
| | - Anastasia Liuzzi
- Department of Life Sciences, University of Parma, 43124, Parma, Italy
| | - Beatrice Fermi
- Department of Life Sciences, University of Parma, 43124, Parma, Italy
| | - Romina Corsini
- Department of Life Sciences, University of Parma, 43124, Parma, Italy
| | - Claudia Folli
- Department of Food Science University of Parma, 43124, Parma, Italy
| | | | | | - Stefano Bettati
- Department of Neurosciences, University of Parma, 43124, Parma, Italy
| | - Luca Ronda
- Department of Neurosciences, University of Parma, 43124, Parma, Italy
| | - Laura Cendron
- Department of Biology, University of Padova, 35121, Padova, Italy
| | - Rodolfo Berni
- Department of Life Sciences, University of Parma, 43124, Parma, Italy
| | - Giuseppe Zanotti
- Department of Biology, University of Padova, 35121, Padova, Italy
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18
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Hicks KA, Yuen ME, Zhen WF, Gerwig TJ, Story RW, Kopp MC, Snider MJ. Structural and Biochemical Characterization of 6-Hydroxynicotinic Acid 3-Monooxygenase, A Novel Decarboxylative Hydroxylase Involved in Aerobic Nicotinate Degradation. Biochemistry 2016; 55:3432-46. [DOI: 10.1021/acs.biochem.6b00105] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Katherine A. Hicks
- Department
of Chemistry, SUNY Cortland, Cortland, New York 13045, United States
| | - Meigan E. Yuen
- Department
of Chemistry, SUNY Cortland, Cortland, New York 13045, United States
| | - Wei Feng Zhen
- Department
of Chemistry, SUNY Cortland, Cortland, New York 13045, United States
| | - Tyler J. Gerwig
- Department
of Chemistry, The College of Wooster, Wooster, Ohio 44691, United States
| | - Ryan W. Story
- Department
of Chemistry, The College of Wooster, Wooster, Ohio 44691, United States
| | - Megan C. Kopp
- Department
of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Mark J. Snider
- Department
of Chemistry, The College of Wooster, Wooster, Ohio 44691, United States
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19
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Baral B, Teixeira da Silva JA, Izaguirre-Mayoral ML. Early signaling, synthesis, transport and metabolism of ureides. JOURNAL OF PLANT PHYSIOLOGY 2016; 193:97-109. [PMID: 26967003 DOI: 10.1016/j.jplph.2016.01.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/04/2015] [Accepted: 01/11/2016] [Indexed: 05/26/2023]
Abstract
The symbiosis between α nitrogen (N2)-fixing Proteobacteria (family Rhizobiaceae) and legumes belonging to the Fabaceae (a single phylogenetic group comprising three subfamilies: Caesalpinioideae, Mimosoideae and Papilionoideae) results in the formation of a novel root structure called a nodule, where atmospheric N2 is fixed into NH3(+). In the determinate type of nodules harbored by Rhizobium-nodulated Fabaceae species, newly synthesized NH3(+) is finally converted into allantoin (C4H6N4O3) and allantoic acid (C4H8N4O4) (ureides) through complex pathways involving at least 20 different enzymes that act synchronously in two types of nodule cells with contrasting ultrastructure, including the tree nodule cell organelles. Newly synthesized ureides are loaded into the network of nodule-root xylem vessels and transported to aerial organs by the transpirational water current. Once inside the leaves, ureides undergo an enzymatically driven reverse process to yield NH4(+) that is used for growth. This supports the role of ureides as key nitrogen (N)-compounds for the growth and yield of legumes nodulated by Rhizobium that grow in soils with a low N content. Thus, a concrete understanding of the mechanisms underlying ureide biogenesis and catabolism in legumes may help agrobiologists to achieve greater agricultural discoveries. In this review we focus on the transmembranal and transorganellar symplastic and apoplastic movement of N-precursors within the nodules, as well as on the occurrence, localization and properties of enzymes and genes involved in the biogenesis and catabolism of ureides. The synthesis and transport of ureides are not unique events in Rhizobium-nodulated N2-fixing legumes. Thus, a brief description of the synthesis and catabolism of ureides in non-legumes was included for comparison. The establishment of the symbiosis, nodule organogenesis and the plant's control of nodule number, synthesis and translocation of ureides via feed-back inhibition mechanisms are also reviewed.
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Affiliation(s)
- Bikash Baral
- Faculty of Agriculture and Forestry, University of Helsinki, P.O. Box 27, Latokartanonkaari 7, FIN-00014 Helsinki, Finland.
| | | | - Maria Luisa Izaguirre-Mayoral
- Biological Nitrogen Fixation Laboratory, Chemistry Department, Faculty of Science, Tshwane University of Technology, Private Bag X680, Pretoria 0001, South Africa.
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20
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Eilers U, Dietzel L, Breitenbach J, Büchel C, Sandmann G. Identification of genes coding for functional zeaxanthin epoxidases in the diatom Phaeodactylum tricornutum. JOURNAL OF PLANT PHYSIOLOGY 2016; 192:64-70. [PMID: 26851888 DOI: 10.1016/j.jplph.2016.01.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 01/15/2016] [Accepted: 01/18/2016] [Indexed: 05/21/2023]
Abstract
Phaeodactylum tricornutum like other diatoms synthesizes fucoxanthin and diadinoxanthin as major carotenoid end products. The genes involved have recently been assigned for early pathway steps. Beyond β-carotene, only gene candidates for β-carotene hydroxylase, zeaxanthin epoxidase and zeaxanthin de-epoxidase have been proposed from the available genome sequence. The two latter enzymes may be involved in the two different xanthophyll cycles which operate in P. tricornutum. The function of three putative zeaxanthin epoxidase genes (zep) was addressed by pathway complementation in the Arabidopsis thaliana Zep mutant npq2. Genes zep2 and zep3 were able to restore zeaxanthin epoxidation and a functional xanthophyll cycle but the corresponding enzymes exhibited different catalytic activities. Zep3 functioned as a zeaxanthin epoxidase whereas Zep2 exhibited a broader substrate specificity additionally converting lutein to lutein-5,6-epoxide. Although zep1 was transcribed and the protein could be identified after import into the chloroplast in A. thaliana, Zep1 was found not to be functional in zeaxanthin epoxidation. The non-photochemical quenching kinetics of wild type A. thaliana was only restored in transformant npq2-zep3.
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Affiliation(s)
- Ulrike Eilers
- Department of Molecular Bioscience, J.W. Goethe University, Max-v-Laue Str. 9, D-60438 Frankfurt, Germany
| | - Lars Dietzel
- Department of Molecular Bioscience, J.W. Goethe University, Max-v-Laue Str. 9, D-60438 Frankfurt, Germany
| | - Jürgen Breitenbach
- Department of Molecular Bioscience, J.W. Goethe University, Max-v-Laue Str. 9, D-60438 Frankfurt, Germany
| | - Claudia Büchel
- Department of Molecular Bioscience, J.W. Goethe University, Max-v-Laue Str. 9, D-60438 Frankfurt, Germany
| | - Gerhard Sandmann
- Department of Molecular Bioscience, J.W. Goethe University, Max-v-Laue Str. 9, D-60438 Frankfurt, Germany.
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21
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The identification of an integral membrane, cytochrome c urate oxidase completes the catalytic repertoire of a therapeutic enzyme. Sci Rep 2015; 5:13798. [PMID: 26349049 PMCID: PMC4562309 DOI: 10.1038/srep13798] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 08/05/2015] [Indexed: 01/24/2023] Open
Abstract
In living organisms, the conversion of urate into allantoin requires three consecutive enzymes. The pathway was lost in hominid, predisposing humans to hyperuricemia and gout. Among other species, the genomic distribution of the two last enzymes of the pathway is wider than that of urate oxidase (Uox), suggesting the presence of unknown genes encoding Uox. Here we combine gene network analysis with association rule learning to identify the missing urate oxidase. In contrast with the known soluble Uox, the identified gene (puuD) encodes a membrane protein with a C-terminal cytochrome c. The 8-helix transmembrane domain corresponds to DUF989, a family without similarity to known proteins. Gene deletion in a PuuD-encoding organism (Agrobacterium fabrum) abolished urate degradation capacity; the phenotype was fully restored by complementation with a cytosolic Uox from zebrafish. Consistent with H2O2 production by zfUox, urate oxidation in the complemented strain caused a four-fold increase of catalase. No increase was observed in the wild-type, suggesting that urate oxidation by PuuD proceeds through cytochrome c-mediated electron transfer. These findings identify a missing link in purine catabolism, assign a biochemical activity to a domain of unknown function (DUF989), and complete the catalytic repertoire of an enzyme useful for human therapy.
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22
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Huijbers MME, Montersino S, Westphal AH, Tischler D, van Berkel WJH. Flavin dependent monooxygenases. Arch Biochem Biophys 2013; 544:2-17. [PMID: 24361254 DOI: 10.1016/j.abb.2013.12.005] [Citation(s) in RCA: 359] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/06/2013] [Accepted: 12/09/2013] [Indexed: 11/29/2022]
Abstract
Flavin-dependent monooxygenases catalyze a wide variety of chemo-, regio- and enantioselective oxygenation reactions. As such, they are involved in key biological processes ranging from catabolism, detoxification and biosynthesis, to light emission and axon guidance. Based on fold and function, flavin-dependent monooxygenases can be distributed into eight groups. Groups A and B comprise enzymes that rely on NAD(P)H as external electron donor. Groups C-F are two-protein systems, composed of a monooxygenase and a flavin reductase. Groups G and H comprise internal monooxygenases that reduce the flavin cofactor through substrate oxidation. Recently, many new flavin-dependent monooxygenases have been discovered. In addition to posing basic enzymological questions, these proteins attract attention of pharmaceutical and fine-chemical industries, given their importance as regio- and enantioselective biocatalysts. In this review we present an update of the classification of flavin-dependent monooxygenases and summarize the latest advances in our understanding of their catalytic and structural properties.
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Affiliation(s)
- Mieke M E Huijbers
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Stefania Montersino
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Adrie H Westphal
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Dirk Tischler
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands; Interdisciplinary Ecological Center, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany
| | - Willem J H van Berkel
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands.
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23
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Scott B, Young CA, Saikia S, McMillan LK, Monahan BJ, Koulman A, Astin J, Eaton CJ, Bryant A, Wrenn RE, Finch SC, Tapper BA, Parker EJ, Jameson GB. Deletion and gene expression analyses define the paxilline biosynthetic gene cluster in Penicillium paxilli. Toxins (Basel) 2013; 5:1422-46. [PMID: 23949005 PMCID: PMC3760044 DOI: 10.3390/toxins5081422] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 07/22/2013] [Accepted: 08/02/2013] [Indexed: 11/16/2022] Open
Abstract
The indole-diterpene paxilline is an abundant secondary metabolite synthesized by Penicillium paxilli. In total, 21 genes have been identified at the PAX locus of which six have been previously confirmed to have a functional role in paxilline biosynthesis. A combination of bioinformatics, gene expression and targeted gene replacement analyses were used to define the boundaries of the PAX gene cluster. Targeted gene replacement identified seven genes, paxG, paxA, paxM, paxB, paxC, paxP and paxQ that were all required for paxilline production, with one additional gene, paxD, required for regular prenylation of the indole ring post paxilline synthesis. The two putative transcription factors, PP104 and PP105, were not co-regulated with the pax genes and based on targeted gene replacement, including the double knockout, did not have a role in paxilline production. The relationship of indole dimethylallyl transferases involved in prenylation of indole-diterpenes such as paxilline or lolitrem B, can be found as two disparate clades, not supported by prenylation type (e.g., regular or reverse). This paper provides insight into the P. paxilli indole-diterpene locus and reviews the recent advances identified in paxilline biosynthesis.
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Affiliation(s)
- Barry Scott
- Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand; E-Mails: (C.A.Y.); (S.S.) (L.K.M.); (B.J.M.); (J.A.); (C.J.E.); (A.B.); (R.E.W.); (E.J.P.); (G.B.J.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +64-6-350-5168; Fax: +64-6-350-5688
| | - Carolyn A. Young
- Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand; E-Mails: (C.A.Y.); (S.S.) (L.K.M.); (B.J.M.); (J.A.); (C.J.E.); (A.B.); (R.E.W.); (E.J.P.); (G.B.J.)
- The Samuel Roberts Noble Foundation, Ardmore, OK 73401, USA
| | - Sanjay Saikia
- Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand; E-Mails: (C.A.Y.); (S.S.) (L.K.M.); (B.J.M.); (J.A.); (C.J.E.); (A.B.); (R.E.W.); (E.J.P.); (G.B.J.)
| | - Lisa K. McMillan
- Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand; E-Mails: (C.A.Y.); (S.S.) (L.K.M.); (B.J.M.); (J.A.); (C.J.E.); (A.B.); (R.E.W.); (E.J.P.); (G.B.J.)
| | - Brendon J. Monahan
- Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand; E-Mails: (C.A.Y.); (S.S.) (L.K.M.); (B.J.M.); (J.A.); (C.J.E.); (A.B.); (R.E.W.); (E.J.P.); (G.B.J.)
| | - Albert Koulman
- AgResearch, Grasslands Research Centre, Private Bag 11 008, Palmerston North 4442, New Zealand; E-Mails: (A.K.); (B.A.T.)
| | - Jonathan Astin
- Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand; E-Mails: (C.A.Y.); (S.S.) (L.K.M.); (B.J.M.); (J.A.); (C.J.E.); (A.B.); (R.E.W.); (E.J.P.); (G.B.J.)
| | - Carla J. Eaton
- Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand; E-Mails: (C.A.Y.); (S.S.) (L.K.M.); (B.J.M.); (J.A.); (C.J.E.); (A.B.); (R.E.W.); (E.J.P.); (G.B.J.)
| | - Andrea Bryant
- Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand; E-Mails: (C.A.Y.); (S.S.) (L.K.M.); (B.J.M.); (J.A.); (C.J.E.); (A.B.); (R.E.W.); (E.J.P.); (G.B.J.)
| | - Ruth E. Wrenn
- Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand; E-Mails: (C.A.Y.); (S.S.) (L.K.M.); (B.J.M.); (J.A.); (C.J.E.); (A.B.); (R.E.W.); (E.J.P.); (G.B.J.)
| | - Sarah C. Finch
- AgResearch, Ruakura Research Centre, East Street, Private Bag 3123, Hamilton 3214, New Zealand; E-Mail:
| | - Brian A. Tapper
- AgResearch, Grasslands Research Centre, Private Bag 11 008, Palmerston North 4442, New Zealand; E-Mails: (A.K.); (B.A.T.)
| | - Emily J. Parker
- Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand; E-Mails: (C.A.Y.); (S.S.) (L.K.M.); (B.J.M.); (J.A.); (C.J.E.); (A.B.); (R.E.W.); (E.J.P.); (G.B.J.)
| | - Geoffrey B. Jameson
- Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand; E-Mails: (C.A.Y.); (S.S.) (L.K.M.); (B.J.M.); (J.A.); (C.J.E.); (A.B.); (R.E.W.); (E.J.P.); (G.B.J.)
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Zhao H, French JB, Fang Y, Benkovic SJ. The purinosome, a multi-protein complex involved in the de novo biosynthesis of purines in humans. Chem Commun (Camb) 2013; 49:4444-52. [PMID: 23575936 DOI: 10.1039/c3cc41437j] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Purine nucleotides are ubiquitous molecules that play vital roles in all kingdoms of life, not only as components of nucleic acids, but also participating in signaling and energy storage. Cellular pools of purines are maintained by the tight control of several complementary and sometimes competing processes including de novo biosynthesis, salvage and catabolism of nucleotides. While great strides have been made over the past sixty years in understanding the biosynthesis of purines, we are experiencing a renaissance in this field. In this feature article we discuss the most recent discoveries relating to purine biosynthesis, with particular emphasis upon the dynamic multi-protein complex called the purinosome. In particular we highlight advances made towards understanding the assembly, control and function of this protein complex and the attempts made to exploit this knowledge for drug discovery.
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Affiliation(s)
- Hong Zhao
- Department of Chemistry, The Pennsylvania State University, 414 Wartik Laboratory, University Park, PA 16802, USA
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